You are in a tough spot because she is choosing he AP over you. You separating while it shows some strength on your part isn't enough to stop the affair. She has no fear of losing you right now.
Your options are:
1. You can work on yourself and be plan B in hope the A fizzles out and maybe she comes back to you. 2. Decide this is BS and you love yourself too much to be someone's plan B and file for divorce.